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- PDB-3rks: Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (... -

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Basic information

Entry
Database: PDB / ID: 3rks
TitleCrystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) K176P mutant
ComponentsHydroxynitrilase
KeywordsLYASE / reversible / stereospecific metabolism / cyanohydrins / natural ligand / acetone / acetate / acetate cyanohydrin
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesManihot esculenta (cassava)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCielo, C.B.C. / Yamane, T. / Asano, Y. / Dadashipour, M. / Suzuki, A. / Mizushima, T. / Komeda, H.
CitationJournal: To be Published
Title: Crystallographic Studies of Manihot esculenta hydroxynitrile lyase Lysine-to-Proline mutants
Authors: Cielo, C.B.C. / Yamane, T. / Asano, Y. / Dadashipour, M. / Suzuki, A. / Mizushima, T. / Komeda, H.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxynitrilase
B: Hydroxynitrilase
C: Hydroxynitrilase
D: Hydroxynitrilase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6916
Polymers117,5064
Non-polymers1842
Water9,134507
1
A: Hydroxynitrilase
C: Hydroxynitrilase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8453
Polymers58,7532
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-12 kcal/mol
Surface area19420 Å2
MethodPISA
2
B: Hydroxynitrilase
D: Hydroxynitrilase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8453
Polymers58,7532
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.628, 91.414, 137.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hydroxynitrilase / / (S)-acetone-cyanohydrin lyase / (S)-hydroxynitrile lyase / Oxynitrilase


Mass: 29376.617 Da / Num. of mol.: 4 / Mutation: K126P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manihot esculenta (cassava) / Gene: HNL / Production host: Escherichia coli (E. coli) / References: UniProt: P52705, EC: 4.1.2.37
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG 400, 2.0M ammonium sulphate, 0.1M Hepes-Na (pH 7.5), 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 38539 / Num. obs: 36063 / % possible obs: 98.5 %

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23819 1895 5 %RANDOM
Rwork0.17399 ---
obs0.17724 36063 98.49 %-
all-38539 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.782 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 12 507 8807
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 124 -
Rwork0.239 2444 -
obs--92.27 %

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